NEW YORK – Researchers have used a "living organoid" biobank to identify two distinct molecular subtypes of Crohn's disease, along with candidate therapeutic molecules targeting each one, in a recent study that may open new avenues for the clinical management of the disease.
Crohn's disease is a complex, heterogenous, and currently incurable disorder characterized by chronic inflammation in the digestive tract and frequently co-occurring complications such as intestinal fibrosis and bowel destruction.
One of the challenges in understanding the disease and developing effecting therapies with which to treat it is that it lacks preclinical animal models that faithfully recapitulate its diverse components.
This dearth of preclinical models has stymied efforts to understand what drives heterogeneity and progression in Crohn's disease and by extension, has left researchers somewhat in the dark when seeking effective therapeutic options. Anti-inflammatory medications currently comprise the primary type of treatment, for instance, but these are imprecise and don't target the underlying factors that trigger inflammation in the first place.
Researchers affiliated with the University of California, San Diego, hypothesized that this challenge might be overcome by establishing a biobank of patient-derived organoid cultures from colonic biopsies. Their work was published last week in Cell Reports Medicine.
The team cultured PDOs from 34 people with Crohn's disease, 10 with ulcerative colitis (another inflammatory bowel disorder), and nine healthy individuals, all of them patients at the UCSD Medical Center.
While PDOs from each subpopulation of patients showed clearly distinct gene expression patterns, RNA sequencing revealed two other transcriptionally distinct clusters of PDOs within the Crohn's disease patients.
In one cluster, genes involved in intestinal infectious diseases, bacterial clearance, and the formation of organ-specific T cells were significantly differentially upregulated, while genes related to interferons, chemokines, and cytokine signaling pathways were differentially downregulated. In contrast, the other cluster was characterized by significantly upregulated genes related to oncogene- and oxidative stress-induced senescence, cellular responses to stress, and defects of apoptosis, while significantly downregulated genes were largely involved in the inhibition of fibrogenic transforming growth factor signals.
Based on these differences, the investigators labeled the two subtypes "immune-deficient infectious Crohn's disease" (IDICD) and "senescence and stress-induced fibrotic Crohn's disease" (S2FCD).
In accordance with their transcriptomic differences, the two subtypes also showed phenotypical differences. IDICD cells, for example, showed higher rates of cellular turnover, owing to increased apoptosis and proliferation. S2FCD cells, in contrast, showed increased rates of senescence, particularly in PDOs from therapy-naïve patients or those who failed to respond to anti-TNF-alpha therapy.
The pronounced differences in subtype led the researchers to ask whether the observed phenotypes could be reversed with subtype-specific therapeutics. They were able to reverse senescence with CTI BioPharma's Vonjo (pacritinib), an anti-cancer medication used to treat myelofibrosis. They successfully reversed the immune deficiency in the case of infection by treating PDOs infected with a pathogenic Escherichia coli strain with Dong-A Pharmaceutical's PAR5359, a dual PPAR-alpha and gamma agonist used to manage type 2 diabetes. Importantly, each drug was unable to reverse the other phenotypes, demonstrating clear subtype specificity.
"This publication is just the start of much more to come," Pradipta Ghosh, director of the Institute for Network Medicine at UCSD and the study's principal investigator, said via email. "The study has raised several intriguing questions, such as how each PDO phenotype relates to how the donor patient fared over long-term follow-up in the clinic."
Ghosh also said that future work will look into whether and how PDO characteristics can be used to predict a patient's clinical trajectory, as well as their response to therapy.
Using whole-genome sequencing, Ghosh is currently looking into whether a gene mutation signature can also identify the two subtypes seen in her recent study.
"If successful, this could lead to a simple point-of-care test to quickly identify a patient's molecular subtype, making precision treatment more accessible and targeted," she said.
UCSD has filed a methods patent covering the approach used in this study. In addition, the Institute for Network Medicine, through its Humanoid Center of Research Excellence, is now developing two drugs geared toward reversing the two newly discovered Crohn's disease subtypes.
Ghosh explained that while these new drug candidates are not the same molecules identified in her study, they target the same functions that are impaired in the two molecular subtypes.
"We are actively working on [these] and believe that [they] are of high commercial value," Ghosh said, adding that she has been approached by several large companies as potential commercialization partners, but that it is too early to reveal which companies those are.
Numerous companies are active in the IBD precision medicine space. Tokyo-based Takeda, for instance, launched its CDPath Crohn's disease prognostic assay in 2022. The test utilizes a patient's disease history along with several genetic and serological markers to rank an individual's three-year risk of developing serious complications. Seattle-based Adaptive Biotechnologies is also fielding its own IBD test through its ImmunoSEQ platform, which profiles Crohn's disease-related T- and B-cell receptor sequences.
More recently, Open Targets and the Wellcome Sanger Institute teamed up to identify biomarkers of IBD onset and severity that might inform precision medicine treatments.
In addition to developing the two drug candidates, Ghosh said that scientists with the Humanoid Center have been able to use patient-derived stromal cells to accurately model and predict what makes some Crohn's disease patients progress to intestinal fibrosis and stricturing disease, while others do not.
"Exciting times lie ahead as we explore these next steps," Ghosh said.